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biocore / micronota

annotation pipeline for microbial genomes and metagenomes
BSD 3-Clause "New" or "Revised" License
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configuration and logging #54

Closed RNAer closed 8 years ago

RNAer commented 8 years ago
mortonjt commented 8 years ago

First pass through. Looking good.

Don't forget to resolve the flake8 error.

mortonjt commented 8 years ago

Still have some pep8 errors ...

mortonjt commented 8 years ago

Can we overhaul the parsing to explicitly handle sam output, rather than blast output in _annotate_fp?

We need all of the uniref sequences that hit, for the cache.

RNAer commented 8 years ago

do u want to add that? just another static function in the class and return pd.DataFrame.

On Tue, Mar 8, 2016 at 10:41 PM, Jamie Morton notifications@github.com wrote:

Can we overhaul the parsing to explicitly handle sam output, rather than blast output.

We need all of the uniref sequences that hit, for the cache.

— Reply to this email directly or view it on GitHub https://github.com/biocore/micronota/pull/54#issuecomment-194140750.

mortonjt commented 8 years ago

Yup. Adding that now.

mortonjt commented 8 years ago

This is still missing tests. Can we have some really basic tests to just run to through the code?

mortonjt commented 8 years ago

Also, note that the tests are a little out-dated, since search_protein_homologs has changed names.

mortonjt commented 8 years ago

First pass through. It think it's ready to merge after these comments are addressed.